Make use of TIFF's ExtraSamples tag
The TIFF file format contains the ExtraSamples tag (338) which can be used to give a description of extra components. This field can be used to specify inside the file if it contains premultiplied or straight data.
When AE exports a TIFF sequence it just leaves this field as UNSPECIFIED. This causes other software (and AE itself) to be unable to know if the data is premultiplied or straight.
Similarly, when a composition is created from a TIFF file AE does not seem to read this field and thus it's guessing wrong as to what kind of contents is in that file.